<HTML>
<HEAD>
<TITLE>g_rmsf</TITLE>
<LINK rel=stylesheet href="style.css" type="text/css">
<BODY text="#000000" bgcolor="#FFFFFF" link="#0000FF" vlink="#990000" alink="#FF0000">
<TABLE WIDTH="98%" NOBORDER >
<TR><TD WIDTH=400>
<TABLE WIDTH=400 NOBORDER>
<TD WIDTH=116>
<a href="http://www.gromacs.org/"><img SRC="../images/gmxlogo_small.png"BORDER=0 </a></td>
<td ALIGN=LEFT VALIGN=TOP WIDTH=280><br><h2>g_rmsf</h2><font size=-1><A HREF="../online.html">Main Table of Contents</A></font><br><br></td>
</TABLE></TD><TD WIDTH="*" ALIGN=RIGHT VALIGN=BOTTOM><p><B>VERSION 4.5<br>
Thu 26 Aug 2010</B></td></tr></TABLE>
<HR>
<H3>Description</H3>
<p>
g_rmsf computes the root mean square fluctuation (RMSF, i.e. standard 
deviation) of atomic positions 
after (optionally) fitting to a reference frame.<p>
With option <tt>-oq</tt> the RMSF values are converted to B-factor
values, which are written to a <a href="pdb.html">pdb</a> file with the coordinates, of the
structure file, or of a <a href="pdb.html">pdb</a> file when <tt>-q</tt> is specified.
Option <tt>-ox</tt> writes the B-factors to a file with the average
coordinates.<p>
With the option <tt>-od</tt> the root mean square deviation with
respect to the reference structure is calculated.<p>
With the option <tt>aniso</tt> g_rmsf will compute anisotropic
temperature factors and then it will also output average coordinates
and a <a href="pdb.html">pdb</a> file with ANISOU records (corresonding to the <tt>-oq</tt>
or <tt>-ox</tt> option). Please note that the U values
are orientation dependent, so before comparison with experimental data
you should verify that you fit to the experimental coordinates.<p>
When a <a href="pdb.html">pdb</a> input file is passed to the program and the <tt>-aniso</tt>
flag is set
a correlation plot of the Uij will be created, if any anisotropic
temperature factors are present in the <a href="pdb.html">pdb</a> file.<p>
With option <tt>-dir</tt> the average MSF (3x3) matrix is diagonalized.
This shows the directions in which the atoms fluctuate the most and
the least.
<P>
<H3>Files</H3>
<TABLE BORDER=1 CELLSPACING=0 CELLPADDING=2>
<TR><TH>option</TH><TH>filename</TH><TH>type</TH><TH>description</TH></TR>
<TR><TD ALIGN=RIGHT> <b><tt>-f</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="files.html">    traj.xtc</a></tt> </TD><TD> Input </TD><TD> Trajectory: <a href="xtc.html">xtc</a> <a href="trr.html">trr</a> <a href="trj.html">trj</a> <a href="gro.html">gro</a> <a href="g96.html">g96</a> <a href="pdb.html">pdb</a> cpt </TD></TR>
<TR><TD ALIGN=RIGHT> <b><tt>-s</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="files.html">   topol.tpr</a></tt> </TD><TD> Input </TD><TD> Structure+mass(db): <a href="tpr.html">tpr</a> <a href="tpb.html">tpb</a> <a href="tpa.html">tpa</a> <a href="gro.html">gro</a> <a href="g96.html">g96</a> <a href="pdb.html">pdb</a> </TD></TR>
<TR><TD ALIGN=RIGHT> <b><tt>-n</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="ndx.html">   index.ndx</a></tt> </TD><TD> Input, Opt. </TD><TD> Index file </TD></TR>
<TR><TD ALIGN=RIGHT> <b><tt>-q</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="pdb.html">   eiwit.pdb</a></tt> </TD><TD> Input, Opt. </TD><TD> Protein data bank file </TD></TR>
<TR><TD ALIGN=RIGHT> <b><tt>-oq</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="pdb.html">    bfac.pdb</a></tt> </TD><TD> Output, Opt. </TD><TD> Protein data bank file </TD></TR>
<TR><TD ALIGN=RIGHT> <b><tt>-ox</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="pdb.html">   xaver.pdb</a></tt> </TD><TD> Output, Opt. </TD><TD> Protein data bank file </TD></TR>
<TR><TD ALIGN=RIGHT> <b><tt>-o</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="xvg.html">    rmsf.xvg</a></tt> </TD><TD> Output </TD><TD> xvgr/xmgr file </TD></TR>
<TR><TD ALIGN=RIGHT> <b><tt>-od</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="xvg.html">  rmsdev.xvg</a></tt> </TD><TD> Output, Opt. </TD><TD> xvgr/xmgr file </TD></TR>
<TR><TD ALIGN=RIGHT> <b><tt>-oc</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="xvg.html">  correl.xvg</a></tt> </TD><TD> Output, Opt. </TD><TD> xvgr/xmgr file </TD></TR>
<TR><TD ALIGN=RIGHT> <b><tt>-dir</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="log.html">    rmsf.log</a></tt> </TD><TD> Output, Opt. </TD><TD> Log file </TD></TR>
</TABLE>
<P>
<H3>Other options</H3>
<TABLE BORDER=1 CELLSPACING=0 CELLPADDING=2>
<TR><TH>option</TH><TH>type</TH><TH>default</TH><TH>description</TH></TR>
<TR><TD ALIGN=RIGHT> <b><tt>-[no]h</tt></b> </TD><TD ALIGN=RIGHT> gmx_bool </TD><TD ALIGN=RIGHT> <tt>no    </tt> </TD><TD> Print help info and quit </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-[no]version</tt></b> </TD><TD ALIGN=RIGHT> gmx_bool </TD><TD ALIGN=RIGHT> <tt>no    </tt> </TD><TD> Print version info and quit </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-nice</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>19</tt> </TD><TD> Set the nicelevel </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-b</tt></b> </TD><TD ALIGN=RIGHT> time </TD><TD ALIGN=RIGHT> <tt>0     </tt> </TD><TD> First frame (ps) to read from trajectory </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-e</tt></b> </TD><TD ALIGN=RIGHT> time </TD><TD ALIGN=RIGHT> <tt>0     </tt> </TD><TD> Last frame (ps) to read from trajectory </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-dt</tt></b> </TD><TD ALIGN=RIGHT> time </TD><TD ALIGN=RIGHT> <tt>0     </tt> </TD><TD> Only use frame when t MOD dt = first time (ps) </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-[no]w</tt></b> </TD><TD ALIGN=RIGHT> gmx_bool </TD><TD ALIGN=RIGHT> <tt>no    </tt> </TD><TD> View output <a href="xvg.html">xvg</a>, <a href="xpm.html">xpm</a>, <a href="eps.html">eps</a> and <a href="pdb.html">pdb</a> files </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-xvg</tt></b> </TD><TD ALIGN=RIGHT> enum </TD><TD ALIGN=RIGHT> <tt>xmgrace</tt> </TD><TD> <a href="xvg.html">xvg</a> plot formatting: <tt>xmgrace</tt>, <tt>xmgr</tt> or <tt>none</tt> </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-[no]res</tt></b> </TD><TD ALIGN=RIGHT> gmx_bool </TD><TD ALIGN=RIGHT> <tt>no    </tt> </TD><TD> Calculate averages for each residue </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-[no]aniso</tt></b> </TD><TD ALIGN=RIGHT> gmx_bool </TD><TD ALIGN=RIGHT> <tt>no    </tt> </TD><TD> Compute anisotropic termperature factors </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-[no]fit</tt></b> </TD><TD ALIGN=RIGHT> gmx_bool </TD><TD ALIGN=RIGHT> <tt>yes   </tt> </TD><TD> Do a least squares superposition before computing RMSF. Without this you must make sure that the reference structure and the trajectory match. </TD></TD>
</TABLE>
<P>
<hr>
<div ALIGN=RIGHT>
<font size="-1"><a href="http://www.gromacs.org">http://www.gromacs.org</a></font><br>
<font size="-1"><a href="mailto:gromacs@gromacs.org">gromacs@gromacs.org</a></font><br>
</div>
</BODY>
